So....@Yllanes over on AA board posted this

https://www.flyertalk.com/forum/36362990-post148.html

So the train still runs! What they called the replacement (we thought bus) is just the same train.

For OP, this means you take the same train from the airport, but then get off at Chamartin, and find a train to Atocha. While NM and C are both big stations with many tracks, I think C is easier as there are many staff to assist pax in finding trains. NM as its name implies is a workplace station without much tourist support.
Between this or the 5 eur bus, for OP, I would still do the bus, despite the train method is back to free (not needing the not free Metro)